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IDH1 isocitrate dehydrogenase (NADP(+)) 1, cytosolic [ Homo sapiens (human) ]

Gene ID: 3417, updated on 9-Sep-2018

Summary

Official Symbol
IDH1provided by HGNC
Official Full Name
isocitrate dehydrogenase (NADP(+)) 1, cytosolicprovided by HGNC
Primary source
HGNC:HGNC:5382
See related
Ensembl:ENSG00000138413 MIM:147700; Vega:OTTHUMG00000132943
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IDH; IDP; IDCD; IDPC; PICD; HEL-216; HEL-S-26
Summary
Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. Each NADP(+)-dependent isozyme is a homodimer. The protein encoded by this gene is the NADP(+)-dependent isocitrate dehydrogenase found in the cytoplasm and peroxisomes. It contains the PTS-1 peroxisomal targeting signal sequence. The presence of this enzyme in peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2, 4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. The cytoplasmic enzyme serves a significant role in cytoplasmic NADPH production. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]
Expression
Ubiquitous expression in adrenal (RPKM 116.0), liver (RPKM 110.2) and 23 other tissues See more
Orthologs

Genomic context

See IDH1 in Genome Data Viewer
Location:
2q34
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (208236227..208255143, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (209100951..209120478, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein SA pseudogene 27 Neighboring gene tumor protein, translationally-controlled 1 pseudogene 2 Neighboring gene IDH1 antisense RNA 1 Neighboring gene phosphoinositide kinase, FYVE-type zinc finger containing Neighboring gene myosin light chain 6B pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of isocitrate dehydrogenase 1 (NADP+), soluble (IDH1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
Knockdown of isocitrate dehydrogenase 1 (NADP+), soluble (IDH1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • 2-Oxocarboxylic acid metabolism, organism-specific biosystem (from KEGG)
    2-Oxocarboxylic acid metabolism, organism-specific biosystem2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate)...
  • 2-Oxocarboxylic acid metabolism, conserved biosystem (from KEGG)
    2-Oxocarboxylic acid metabolism, conserved biosystem2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate)...
  • Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate, organism-specific biosystem (from REACTOME)
    Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate, organism-specific biosystemSomatic mutations affecting arginine residue 132 of IDH1 (isocitrate dehydrogenase 1, a cytosolic enzyme that normally catalyzes the NADP+-dependent conversion of isocitrate to 2-oxoglutarate), are v...
  • Amino Acid metabolism, organism-specific biosystem (from WikiPathways)
    Amino Acid metabolism, organism-specific biosystemA complete overview of the metabolism of all 20 amino acids
  • Biosynthesis of amino acids, organism-specific biosystem (from KEGG)
    Biosynthesis of amino acids, organism-specific biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Biosynthesis of amino acids, conserved biosystem (from KEGG)
    Biosynthesis of amino acids, conserved biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Carbon metabolism, organism-specific biosystem (from KEGG)
    Carbon metabolism, organism-specific biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Carbon metabolism, conserved biosystem (from KEGG)
    Carbon metabolism, conserved biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Central carbon metabolism in cancer, organism-specific biosystem (from KEGG)
    Central carbon metabolism in cancer, organism-specific biosystemMalignant transformation of cells requires specific adaptations of cellular metabolism to support growth and survival. In the early twentieth century, Otto Warburg established that there are fundamen...
  • Central carbon metabolism in cancer, conserved biosystem (from KEGG)
    Central carbon metabolism in cancer, conserved biosystemMalignant transformation of cells requires specific adaptations of cellular metabolism to support growth and survival. In the early twentieth century, Otto Warburg established that there are fundamen...
  • Citrate cycle (TCA cycle), organism-specific biosystem (from KEGG)
    Citrate cycle (TCA cycle), organism-specific biosystemThe citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form ...
  • Citrate cycle (TCA cycle), conserved biosystem (from KEGG)
    Citrate cycle (TCA cycle), conserved biosystemThe citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form ...
  • Citrate cycle (TCA cycle, Krebs cycle), organism-specific biosystem (from KEGG)
    Citrate cycle (TCA cycle, Krebs cycle), organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Citrate cycle (TCA cycle, Krebs cycle), conserved biosystem (from KEGG)
    Citrate cycle (TCA cycle, Krebs cycle), conserved biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, organism-specific biosystem (from KEGG)
    Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, conserved biosystem (from KEGG)
    Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Cytosine methylation, organism-specific biosystem (from WikiPathways)
    Cytosine methylation, organism-specific biosystemDNA, namely cytosine, methylation is the key event in epigentics. The degree of methylation influences gene expression and methylation disorders are known to be major causes of some diseases like Ret...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of metabolism, organism-specific biosystem (from REACTOME)
    Diseases of metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Glutathione metabolism, organism-specific biosystem (from KEGG)
    Glutathione metabolism, organism-specific biosystem
    Glutathione metabolism
  • Glutathione metabolism, conserved biosystem (from KEGG)
    Glutathione metabolism, conserved biosystem
    Glutathione metabolism
  • Glutathione metabolism, organism-specific biosystem (from WikiPathways)
    Glutathione metabolism, organism-specific biosystem
    Glutathione metabolism
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • NADPH regeneration, organism-specific biosystem (from REACTOME)
    NADPH regeneration, organism-specific biosystemThe conversion of isocitrate to 2-oxoglutarate (alpha-ketoglutarate) with the concomitant synthesis of NADPH from NADP+ is thought to play a significant role in supplying NADPH for other reactions in...
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Peroxisomal lipid metabolism, organism-specific biosystem (from REACTOME)
    Peroxisomal lipid metabolism, organism-specific biosystemIn humans, the catabolism of phytanate, pristanate, and very long chain fatty acids as well as the first four steps of the biosynthesis of plasmalogens are catalyzed by peroxisomal enzymes. Defects i...
  • Peroxisome, organism-specific biosystem (from KEGG)
    Peroxisome, organism-specific biosystemPeroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contribute to many crucial metabolic processes such as fatty acid oxidation, biosynthesis of ...
  • Peroxisome, conserved biosystem (from KEGG)
    Peroxisome, conserved biosystemPeroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contribute to many crucial metabolic processes such as fatty acid oxidation, biosynthesis of ...
  • TCA Cycle and Deficiency of Pyruvate Dehydrogenase complex (PDHc), organism-specific biosystem (from WikiPathways)
    TCA Cycle and Deficiency of Pyruvate Dehydrogenase complex (PDHc), organism-specific biosystem
    TCA Cycle and Deficiency of Pyruvate Dehydrogenase complex (PDHc)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
(R)-2-hydroxyglutarate dehydrogenase activity EXP
Inferred from Experiment
more info
PubMed 
NAD binding IEA
Inferred from Electronic Annotation
more info
 
NADP binding IEA
Inferred from Electronic Annotation
more info
 
cadherin binding HDA PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
isocitrate dehydrogenase (NADP+) activity EXP
Inferred from Experiment
more info
PubMed 
isocitrate dehydrogenase (NADP+) activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
isocitrate dehydrogenase (NADP+) activity IDA
Inferred from Direct Assay
more info
PubMed 
magnesium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
protein homodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
2-oxoglutarate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
2-oxoglutarate metabolic process TAS
Traceable Author Statement
more info
 
NADP metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NADPH regeneration TAS
Traceable Author Statement
more info
 
female gonad development IEA
Inferred from Electronic Annotation
more info
 
glutathione metabolic process IEA
Inferred from Electronic Annotation
more info
 
glyoxylate cycle IEA
Inferred from Electronic Annotation
more info
 
isocitrate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
isocitrate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
protein targeting to peroxisome TAS
Traceable Author Statement
more info
 
regulation of phospholipid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of phospholipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
regulation of phospholipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of phospholipid catabolic process IEA
Inferred from Electronic Annotation
more info
 
response to oxidative stress IEA
Inferred from Electronic Annotation
more info
 
response to steroid hormone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to steroid hormone IEA
Inferred from Electronic Annotation
more info
 
tricarboxylic acid cycle IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
peroxisomal matrix TAS
Traceable Author Statement
more info
 
peroxisome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
peroxisome IDA
Inferred from Direct Assay
more info
PubMed 
secretory granule lumen TAS
Traceable Author Statement
more info
 
tertiary granule lumen TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
isocitrate dehydrogenase [NADP] cytoplasmic
Names
NADP(+)-specific ICDH
NADP-dependent isocitrate dehydrogenase, cytosolic
NADP-dependent isocitrate dehydrogenase, peroxisomal
epididymis luminal protein 216
epididymis secretory protein Li 26
isocitrate dehydrogenase 1 (NADP+), soluble
oxalosuccinate decarboxylase
NP_001269315.1
NP_001269316.1
NP_005887.2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023319.2 RefSeqGene

    Range
    15932..34848
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_610

mRNA and Protein(s)

  1. NM_001282386.1NP_001269315.1  isocitrate dehydrogenase [NADP] cytoplasmic

    See identical proteins and their annotated locations for NP_001269315.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC021046, DA707595, N21575
    Consensus CDS
    CCDS2381.1
    UniProtKB/Swiss-Prot
    O75874
    UniProtKB/TrEMBL
    V9HWJ2
    Related
    ENSP00000410513.1, OTTHUMP00000206464, ENST00000446179.5, OTTHUMT00000336670
    Conserved Domains (1) summary
    PTZ00435
    Location:1411
    PTZ00435; isocitrate dehydrogenase; Provisional
  2. NM_001282387.1NP_001269316.1  isocitrate dehydrogenase [NADP] cytoplasmic

    See identical proteins and their annotated locations for NP_001269316.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC012846, DR158630, N21575
    Consensus CDS
    CCDS2381.1
    UniProtKB/Swiss-Prot
    O75874
    UniProtKB/TrEMBL
    V9HWJ2
    Related
    ENSP00000390265.1, OTTHUMP00000206466, ENST00000415913.5, OTTHUMT00000336672
    Conserved Domains (1) summary
    PTZ00435
    Location:1411
    PTZ00435; isocitrate dehydrogenase; Provisional
  3. NM_005896.3NP_005887.2  isocitrate dehydrogenase [NADP] cytoplasmic

    See identical proteins and their annotated locations for NP_005887.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) and variants 2 and 3 encode the same protein.
    Source sequence(s)
    BC021046, DA728868, N21575
    Consensus CDS
    CCDS2381.1
    UniProtKB/Swiss-Prot
    O75874
    UniProtKB/TrEMBL
    V9HWJ2
    Related
    ENSP00000260985.2, OTTHUMP00000163870, ENST00000345146.6, OTTHUMT00000256475
    Conserved Domains (1) summary
    PTZ00435
    Location:1411
    PTZ00435; isocitrate dehydrogenase; Provisional

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    208236227..208255143 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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